Strain identifier

BacDive ID: 7997

Type strain: Yes

Species: Micromonospora coriariae

Strain Designation: NAR01

Strain history: CIP <- 2006, DSMZ <- M.E. Trujillo, Salamanca Univ., Salamanca, Spain: strain NAR01

NCBI tax ID(s): 285665 (species)

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General

@ref: 12162

BacDive-ID: 7997

DSM-Number: 44875

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, Gram-positive

description: Micromonospora coriariae NAR01 is an obligate aerobe, spore-forming, Gram-positive bacterium that was isolated from root nodules of Coriaria sp..

NCBI tax id

  • NCBI tax id: 285665
  • Matching level: species

strain history

@refhistory
12162<- M. E. Trujillo; NAR01
67770LMG 23557 <-- M. E. Trujillo NAR01.
118751CIP <- 2006, DSMZ <- M.E. Trujillo, Salamanca Univ., Salamanca, Spain: strain NAR01

doi: 10.13145/bacdive7997.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora coriariae
  • full scientific name: Micromonospora coriariae Trujillo et al. 2006

@ref: 12162

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora coriariae

full scientific name: Micromonospora coriariae Trujillo et al. 2006

strain designation: NAR01

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118751positiverod-shapedno
69480positive91.355

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12162N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
12162GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
37545MEDIUM 56 - for Micromonospora purpureayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (10.000g);Yeast extract (5.000 g);Starch maize (20.000 g);Calcium carbonate (1.000 g);Casamino acids (5.000 g)
118751CIP Medium 56yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56

culture temp

@refgrowthtypetemperature
12162positivegrowth28
37545positivegrowth30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 118751
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69480yes91.983
69481yes100

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-9(H4), MK-10(H6)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose+builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
118751nitrate+reduction17632
118751nitrite-reduction16301

metabolite production

  • @ref: 118751
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118751oxidase+
118751catalase+1.11.1.6
118751urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118751-+++-++++-++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118751+--+++---++++----+-+/-++++++++++++------++-+----+/---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12162root nodules of Coriaria sp.CoriariaSalamancaSpainESPEurope
67770Root nodules of Coriaria myrtifoliaCoriaria myrtifoliaSalamancaSpainESPEurope
118751Plant, Root nodules of CoriariaSalamancaSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree
#Host Body-Site#Plant#Root nodule

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121621Risk group (German classification)
1187511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12162
  • description: Micromonospora coriariae partial 16S rRNA gene, type strain NAR01T
  • accession: AJ784008
  • length: 1451
  • database: nuccore
  • NCBI tax ID: 285665

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora coriariae DSM 44875GCA_900091455chromosomencbi285665
66792Micromonospora coriariae strain DSM 44875285665.4completepatric285665
66792Micromonospora coriariae DSM 448752623620612draftimg285665

GC content

@refGC-contentmethod
6777071.76genome sequence analysis
6777070.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.355no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.382yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes91.983no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.703yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95no
69480flagellatedmotile2+Ability to perform flagellated movementno86.5no

External links

@ref: 12162

culture collection no.: DSM 44875, CIP 109402, LMG 23557, NRRL B-24772, JCM 14921, NBRC 106140

straininfo link

  • @ref: 77427
  • straininfo: 290941

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012566Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia.Trujillo ME, Kroppenstedt RM, Schumann P, Carro L, Martinez-Molina EInt J Syst Evol Microbiol10.1099/ijs.0.64449-02006Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Magnoliopsida/*microbiology, Micromonospora/classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny22286910Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum.Carro L, Pukall R, Sproer C, Kroppenstedt RM, Trujillo MEInt J Syst Evol Microbiol10.1099/ijs.0.038695-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peas/*microbiology, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analysisGenetics
Phylogeny31395106Micromonospora acroterricola sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil.Carro L, Golinska P, Nouioui I, Bull AT, Igual JM, Andrews BA, Klenk HP, Goodfellow MInt J Syst Evol Microbiol10.1099/ijsem.0.0036342019*Altitude, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Chile, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Micromonospora/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
12162Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44875)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44875
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
37545Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7140
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290941.1StrainInfo: A central database for resolving microbial strain identifiers
118751Curators of the CIPCollection of Institut Pasteur (CIP 109402)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109402